RNA-protein interactions govern many fundamental cellular processes. Recent computational advances have made it now possible to study the interactions of RNA and protein complexes, such as U1A-RNA. The crystal structure of U1A bound to a hairpin RNA has been solved and a NMR structure of U1A bound to an internal-loop RNA has also been determined. We have simulated both structures using molecular dynamics (MD). The goals of the project are 1) to compare the dynamics of the two complexes and understand how U1A binds two different RNAs at sub-nanomolar affinities; 2) model the free hairpin RNA; 3) use free energy calculations to understand the specificity determinants of U1A-RNA. We have used the Computer Graphics Laboratory (CGL) facilities to analyze our simulations. Using MidasPlus, we can view the structures and gain insights on the conformational changes that occur over the MD simulation. Moreover, we have made a movie of the free RNA simulation using CGL resources and presented it at the 1997 Ford Foundation Annual Conference.